Annotating genes and genomes with DNA sequences extracted from biomedical articles.

ABSTRACT:

Motivation

Increasing rates of publication and DNA sequencing make the problem of finding relevant articles for a particular gene or genomic region more challenging than ever. Existing text-mining approaches focus on finding gene names or identifiers in English text. These are often not unique and do not identify the exact genomic location of a study.

Results

Here, we report the results of a novel text-mining approach that extracts DNA sequences from biomedical articles and automatically maps them to genomic databases. We find that ∼20% of open access articles in PubMed central (PMC) have extractable DNA sequences that can be accurately mapped to the correct gene (91%) and genome (96%). We illustrate the utility of data extracted by text2genome from more than 150 000 PMC art

SUBMITTER: Haeussler M 

PROVIDER: S-EPMC3065681 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature